Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Cell & Tissue Engineering
Jonas Simon Fleck, Fatima Sanchis-Calleja, Zhisong He, Malgorzata Santel, Michael James Boyle, J. Gray Camp, Barbara Treutlein
Summary: Complex 3D models resembling brain structures generated from human stem cells provide exciting possibilities for studying brain development, disease, and evolution. However, understanding the heterogeneity observed within and between individual organoids remains a major challenge. Researchers have developed a computational tool (VoxHunt) to assess brain organoid patterning, developmental state, and cell identity through comparisons to spatial and single-cell transcriptome reference datasets.
Article
Biochemistry & Molecular Biology
Jialu Hu, Mengjie Chen, Xiang Zhou
Summary: VIPCCA is a computational framework based on non-linear canonical correlation analysis for effective and scalable single cell data alignment. It combines deep learning for effective single cell data modeling and variational inference for scalable computation, enabling accurate alignment tasks across multiple samples and data types. VIPCCA is suitable for large-scale single cell analysis and can accommodate millions of cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Joseph F. Cardiello, Alberto Joven Araus, Sarantis Giatrellis, Clement Helsens, Andras Simon, Nicholas Leigh
Summary: Single-cell sequencing (sc-seq) is a useful tool for studying cellular processes, but its high cost and the need for sufficient cell quantities and replicates pose challenges. One option is pooling cells from multiple individuals into one sc-seq library. In this study, we validate the application of genotype-based demultiplexing for pooled sc-seq data across non-isogenic model organisms, identifying limitations and demonstrating its potential benefits.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biotechnology & Applied Microbiology
Jian-Rong Li, Mabel Tang, Yafang Li, Christopher Amos, Chao Cheng
Summary: In this study, a computational framework was proposed to infer mRNA stability of genes using RNA-seq data and identify stQTLs. The results revealed that stQTLs were enriched in the CDS and 3'UTR regions, while eQTLs were enriched in multiple regions. Additionally, stQTLs were more likely to overlap with RNA binding protein and microRNA binding sites. This study demonstrates that simultaneous identification of stQTLs and eQTLs provides more mechanistic insight into the association between genetic variants and gene expression levels.
Article
Biotechnology & Applied Microbiology
Zhi-Jie Cao, Ge Gao
Summary: GLUE is a computational framework that bridges the gap between different omics layers by modeling regulatory interactions, and it outperforms state-of-the-art tools in accuracy, robustness, and scalability for heterogeneous single-cell multi-omics data. It has been successfully applied in various challenging tasks.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
Summary: scBalance is an integrated sparse neural network framework that incorporates adaptive weight sampling and dropout techniques to handle noise and imbalanced datasets, achieving high classification accuracy for both rare and major cell types.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Lei Yu, Xinlei Wang, Quanhua Mu, Sindy Sing Ting Tam, Danson Shek Chun Loi, Aden K. Y. Chan, Wai Sang Poon, Ho-Keung Ng, Danny T. M. Chan, Jiguang Wang, Angela Ruohao Wu
Summary: Single-cell multi-omics provides a unique perspective on tumor cellular heterogeneity. We developed scONE-seq, a versatile method for single-cell whole-genome RNA sequencing that is compatible with frozen biobanked samples. By comparing with existing methods, we demonstrated the performance of scONE-seq in various aspects and identified a unique transcriptionally normal-like tumor clone in a frozen astrocytoma sample, suggesting the potential of scONE-seq in uncovering previously unidentified discoveries in tumor biology.
Article
Biotechnology & Applied Microbiology
Ya-Hong Cao, Jie Ding, Qing-Hai Tang, Jie Zhang, Zhong-Yan Huang, Xiao-Mei Tang, Ji-Bin Liu, Yu-Shui Ma, Da Fu
Summary: A tumor's heterogeneity is crucial for understanding its origin, progression, stemness, and drug resistance. Single-cell sequencing (scRNA-seq) technology enables researchers to track gene expression, mutations, and evolution in heterogeneous tumor cells, providing a better understanding of the molecular mechanisms driving tumor growth. Recent advancements in scRNA-seq have opened up new strategies for cancer treatment.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Oncology
Lei Chang, Enze Deng, Jun Wang, Wei Zhou, Jian Ao, Rong Liu, Dan Su, Xiaoying Fan
Summary: Researchers developed a single-cell multi-omics sequencing method called scGTP-seq to analyze ecDNA and SVs, and demonstrated how these variations affect transcriptomic changes in different cell lines. The application of this method in a clinical sample of hepatocellular carcinoma (HCC) validated its feasibility in monitoring the evolution of ecDNA and SVs during cancer progression.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Evolutionary Biology
Navya Shukla, Bobbie Shaban, Irene Gallego Romero
Summary: The research found that current chimpanzee transcriptomic data capture low levels of genetic diversity, with the majority of samples having Western chimpanzee ancestry. Utilizing multiple population genetics approaches, the study identified multiple genetically distinct individuals within the data.
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Plant Sciences
Lijun Li, Qingfeng Zheng, Wei Jiang, Nayun Xiao, Fanrong Zeng, Guang Chen, Michelle Mak, Zhong-Hua Chen, Fenglin Deng
Summary: The sustainable production of crops is challenged by abiotic stressors such as drought, salinity, and toxic metals. Cytokinins play a crucial role in normal development and stress responses in plants. This study summarizes the molecular mechanisms of cytokinins, including biosynthesis, metabolism, transport, and signaling pathways, and explores their functions in salt stress and mineral-toxicity tolerance.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Wei Jiang, Tao Tong, Wen Li, Zhenghong Huang, Guang Chen, Fanrong Zeng, Adeel Riaz, Hanna Amoanimaa-Dede, Rui Pan, Wenying Zhang, Fenglin Deng, Zhong-Hua Chen
Summary: This study investigates the molecular evolution, expression pattern, and physiological functions of 14-3-3 proteins in response to drought stress. The results demonstrate the highly conserved and early evolution of 14-3-3s in green plants and the duplication and expansion of 14-3-3s in angiosperms. The findings also highlight the crucial role of Hv14-3-3s in the rapid stomatal response to drought in barley. This research provides valuable evolutionary and molecular evidence for breeding drought-tolerant crops in a changing global climate.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Nian-Hong Wang, Xue-Yi Zhou, Shou-Heng Shi, Shuo Zhang, Zhong-Hua Chen, Mohamed Abdelalim Ali, Imrul Mosaddek Ahmed, Yizhou Wang, Feibo Wu
Summary: Cadmium (Cd) is a detrimental heavy metal pollutant that has negative effects on crop production and human health. This study identified a Cd-induced miRNA, miR156g-3p_3, that targets HvNAT2 and found that overexpression of HvNAT2 enhances Cd tolerance and reduces oxidative damage in transgenic barley plants. This research provides valuable insights into the molecular mechanism of NAT in Cd tolerance and has implications for sustainable agricultural production and environmental management.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Plant Sciences
Yuanyuan Wang, Guang Chen, Fanrong Zeng, Zhigang Han, Cheng-Wei Qiu, Meng Zeng, Zujun Yang, Fei Xu, Dezhi Wu, Fenglin Deng, Shengchun Xu, Caspar Chater, Abraham Korol, Sergey Shabala, Feibo Wu, Peter Franks, Eviatar Nevo, Zhong-Hua Chen
Summary: This study assessed the natural variation of drought tolerance in wild cereal crops and found that different growth conditions have shaped the stomatal and photosynthetic traits of these crops differently. The research identified specific genes correlated with these differences and verified their role in drought tolerance. These findings provide valuable genetic information for breeding resilient wheat and barley in the face of a changing global climate.
Article
Plant Sciences
Xiaoyuan Tao, Shouli Feng, Sujuan Li, Guang Chen, Jian Wang, Lizhi Xu, Xujun Fu, Jing Yu, Shengchun Xu
Summary: The dU-Tn5 method is a user-friendly and comparable quality strand-specific RNA sequencing protocol, which can be used for the discovery of novel transcripts, genome annotation, and gene expression level profiling.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Fatemeh Rasouli, Ali Kiani-Pouya, Ali Movahedi, Yuan Wang, Leiting Li, Min Yu, Mohammad Pourkheirandish, Meixue Zhou, Zhonghua Chen, Heng Zhang, Sergey Shabala
Summary: A comparative investigation was conducted to evaluate transcriptional changes in guard cells (GCs) of halophytic (Chenopodium quinoa) and glycophytic (Spinacia oleracea) species under salt stress. Salt-responsive genes in both species were mainly related to protein metabolism, secondary metabolites, signal transduction, and transport systems. Quinoa exhibited strong induction of genes related to abscisic acid signaling and biosynthesis, as well as transporters for amino acids, proline, sugars, sucrose, and potassium. Additionally, changes in cell wall-related genes and stomatal development were observed, suggesting that these variations may contribute to the higher salt tolerance and water use efficiency in quinoa.
PLANT AND CELL PHYSIOLOGY
(2023)
Review
Plant Sciences
Ali Raza, Muhammad Salman Mubarik, Rahat Sharif, Madiha Habib, Warda Jabeen, Chong Zhang, Hua Chen, Zhong-Hua Chen, Kadambot H. M. Siddique, Weijian Zhuang, Rajeev K. Varshney
Summary: Breeding crop plants with increased yield potential and improved tolerance to drought stress is crucial for global food security. Understanding the physiological, biochemical, molecular, and ecological mechanisms associated with drought stress is essential. Suboptimal water sources negatively impact crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. Mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods can help control the detrimental effects of drought stress and develop drought-smart cultivars.
Review
Food Science & Technology
Mursleen Yasin, Li Li, Michelle Donovan-Mak, Zhong-Hua Chen, Sunil K. K. Panchal
Summary: Capsaicinoids are compounds with various beneficial properties, such as antioxidants, anti-microbial, anti-inflammatory and anti-diabetic effects. They are synthesized in the placenta of fruits and can be extracted from fruit wastes and plant biowaste. Capsaicin and dihydrocapsaicin are the most abundant capsaicinoids. These compounds have the potential to reduce complications of metabolic diseases. However, the development of safe and effective oral capsaicinoid formulations requires addressing challenges related to dosage, bioavailability, adverse effects, and receptor antagonists.
Article
Food Science & Technology
Zuhaib Siddiqui, Dharmappa Hagare, Min-Hang Liu, Orousa Panatta, Tanveer Hussain, Sheeraz Memon, Amber Noorani, Zhong-Hua Chen
Summary: This study compared the macronutrients and cation concentrations in lettuce, cucumber, and cherry tomatoes grown with food waste-derived liquid fertiliser (FoodLift) and commercial liquid fertiliser (CLF) under hydroponic conditions. The results showed that the nitrogen (N) and phosphorus (P) concentrations were similar between FoodLift and CLF in lettuce and cucumber, but varied in cherry tomatoes. Additionally, the cation concentrations differed between FoodLift and CLF in plants. Overall, FoodLift has the potential to replace CLF in hydroponic systems for lettuce and cucumber.
Article
Environmental Sciences
Shuo Zhang, Chulong Zhang, Zi-Feng Gao, Cheng-Wei Qiu, Shou-Heng Shi, Zhong-Hua Chen, Mohamed Abdelalim Ali, Feng Wang, Feibo Wu
Summary: In this study, the researchers investigated the efficacy of a novel fungal strain, Tricho-derma nigricans T32781, in alleviating cadmium (Cd)-induced stress in tobacco plants. They found that T32781 inoculation led to reduced Cd uptake, alleviation of oxidative stress, and improved plant metabolism. Additionally, they observed an increase in beneficial microbes in the rhizosphere, which contributed to the restoration of plant growth. These findings highlight the importance of T32781 in enhancing Cd tolerance and reducing health risks associated with Cd-contaminated plants.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Plant Sciences
Xin He, Celymar A. Solis, Sachin G. Chavan, Chelsea Maier, Yuanyuan Wang, Weiguang Liang, Norbert Klause, Oula Ghannoum, Christopher I. Cazzonelli, David T. Tissue, Zhong-Hua Chen
Summary: This study investigated the effects of light-blocking films (LBFs) on the transcriptome of orange color capsicum fruits and found significant changes in metabolite percentages. The response of the fruits to LBF treatment differed at 35 and 65 days after pollination, involving multiple biological processes and key gene regulations.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Horticulture
Fatemeh Rasouli, Mohammad Babla, Lihua Li, Weiguang Liang, Miing-Tiem Yong, Talaat Ahmed, David Tissue, Samsul Huda, Zhong-Hua Chen
Summary: This study focused on the physiological traits and productivity of three eggplant cultivars in a high-tech glasshouse. The results showed that the cultivar Tracey had higher leaf growth and number of flowers per node compared to the other two varieties. Despite having the lowest net CO2 assimilation, Tracey produced the highest yield and better water use efficiency in terms of agronomic performance. However, further research is needed to understand the varietal performance of greenhouse eggplants and establish benchmarks for large-scale sustainable production.
Meeting Abstract
Horticulture
Bello Adewale Suraj, Mohammed Alsafran, Samsul Huda, Zhonghua Chen, Talaat Ahmed
Review
Plant Sciences
Xi Chen, Chenchen Zhao, Ping Yun, Min Yu, Meixue Zhou, Zhong-Hua Chen, Sergey Shabala
Summary: Developing climate-resilient crops is crucial for food security and sustainable agriculture. This study compares key traits between drought-tolerant and mesophytic plants to gain genetic insights for improving crop tolerance. The research highlights the importance of changing breeding practices and identifies traits that contribute to drought and salt tolerance.
